The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Xinxia Peng; Jessica Alföldi; Kevin Gori; Amie J Eisfeld; Scott R Tyler; Jennifer Tisoncik-Go; David Brawand; G Lynn Law; Nives Skunca; Masato Hatta; David J Gasper; Sara M Kelly; Jean Chang; Matthew J Thomas; Jeremy Johnson; Aaron M Berlin; Marcia Lara; Pamela Russell; Ross Swofford; Jason Turner-Maier; Sarah Young; Thibaut Hourlier; Bronwen Aken; Steve Searle; Xingshen Sun; Yaling Yi; M Suresh; Terrence M Tumpey; Adam Siepel; Samantha M Wisely; Christophe Dessimoz; Yoshihiro Kawaoka; Bruce W Birren; Kerstin Lindblad-Toh; Federica Di Palma; John F Engelhardt; Robert E Palermo; Michael G Katze

doi:10.1038/nbt.3079

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

Nat Biotechnol. 2014 Dec;32(12):1250-5. doi: 10.1038/nbt.3079. Epub 2014 Nov 17.

Authors

Xinxia Peng¹, Jessica Alföldi², Kevin Gori³, Amie J Eisfeld⁴, Scott R Tyler⁵, Jennifer Tisoncik-Go¹, David Brawand⁶, G Lynn Law¹, Nives Skunca⁷, Masato Hatta⁴, David J Gasper⁴, Sara M Kelly¹, Jean Chang¹, Matthew J Thomas¹, Jeremy Johnson², Aaron M Berlin², Marcia Lara⁶, Pamela Russell⁶, Ross Swofford², Jason Turner-Maier², Sarah Young², Thibaut Hourlier⁸, Bronwen Aken⁸, Steve Searle⁸, Xingshen Sun⁹, Yaling Yi⁹, M Suresh⁴, Terrence M Tumpey¹⁰, Adam Siepel¹¹, Samantha M Wisely¹², Christophe Dessimoz¹³, Yoshihiro Kawaoka¹⁴, Bruce W Birren², Kerstin Lindblad-Toh¹⁵, Federica Di Palma⁶, John F Engelhardt¹⁶, Robert E Palermo¹, Michael G Katze¹⁷

Affiliations

¹ Department of Microbiology, University of Washington, Seattle, Washington, USA.
² Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
³ European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
⁴ Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA.
⁵ 1] Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA. . [2] Molecular and Cellular Biology Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
⁶ 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] MRC Functional Genomics Unit, University of Oxford, xford, UK (D.B.); Biogen Idec, Cambridge, Massachusetts, USA (M.L.); Division of Biology, California Institute of Technology, Pasadena, California, USA (P.R.); Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK (F.D.P.).
⁷ 1] Department of Computer Science, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland. [2] Swiss Institute of Bioinformatics, Zurich, Switzerland.
⁸ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
⁹ Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA. .
¹⁰ Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹¹ Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.
¹² Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA.
¹³ 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. [2] Department of Genetics, Evolution and Environment, University College London, London, UK. [3] Department of Computer Science, University College London, London, UK.
¹⁴ 1] Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA. [2] ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama, Japan. [3] Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. [4] Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan. [5] Laboratory of Bioresponses Regulation, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto, Japan.
¹⁵ 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
¹⁶ 1] Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA. . [2] Center for Gene Therapy, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
¹⁷ 1] Department of Microbiology, University of Washington, Seattle, Washington, USA. [2] Washington National Primate Research Center, Seattle, Washington, USA.

Abstract

The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Chromosome Mapping
Disease Models, Animal
Ferrets / genetics*
Genome*
High-Throughput Nucleotide Sequencing
Humans
Influenza, Human / genetics*
Influenza, Human / transmission
Influenza, Human / virology
Molecular Sequence Annotation
Molecular Sequence Data
Orthomyxoviridae / genetics
Orthomyxoviridae / pathogenicity
Sequence Analysis, DNA*

Associated data

BioProject/PRJNA59869
BioProject/PRJNA78317
GENBANK/AEYP00000000
GEO/GSE49060
GEO/GSE49061
SRA/SRP033621

Abstract

Publication types

MeSH terms

Associated data

Grants and funding